Contacts of the helix formed by residues 679 - 686 (chain C) in PDB entry 5Y7K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 679 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596C ARG* 3.0 44.6 + - - +
671C MET* 2.8 44.2 + - - +
673C LEU 3.2 9.2 + - - +
675C THR 3.2 0.8 + - - -
678C ASP* 1.3 81.0 - - - +
680C LEU* 1.3 68.5 + - - +
681C ASP* 3.0 5.0 + - - +
682C HIS* 3.2 30.7 + - - +
683C TYR* 3.2 10.9 + - + -
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Residues in contact with LEU 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660C GLU* 4.1 6.3 - - - +
673C LEU 4.0 1.0 + - - -
674C PRO* 3.3 24.0 - - + +
675C THR 3.1 20.0 + - - +
676C PRO* 3.6 34.8 + - + +
678C ASP 3.9 0.2 - - - -
679C ASN* 1.3 76.4 - - - +
681C ASP* 1.3 67.3 + - - +
683C TYR* 3.3 5.0 + - + -
684C ARG* 3.1 63.9 + - + +
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Residues in contact with ASP 681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C PRO* 5.7 4.3 - - - +
679C ASN* 3.0 2.3 + - - +
680C LEU* 1.3 82.9 - - - +
682C HIS* 1.3 63.1 + - + +
684C ARG* 3.3 5.9 + - - +
685C ASN* 2.9 34.3 + - - +
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Residues in contact with HIS 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C ARG* 2.4 34.7 + - + +
597C ARG* 3.9 28.1 + - + +
598C LEU 6.1 0.2 - - - +
600C THR* 6.0 3.8 - - + +
671C MET* 3.7 11.4 - - + +
679C ASN* 3.2 21.3 + - - +
681C ASP* 1.3 84.0 - - + +
683C TYR* 1.3 60.2 + - - +
685C ASN* 4.1 9.1 - - + +
686C SER* 2.9 30.7 + - - -
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Residues in contact with TYR 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ALA* 3.9 20.6 - - + +
659C TRP* 3.8 22.6 + - + -
660C GLU* 3.7 31.5 - - + +
667C THR* 3.4 30.4 - - + +
668C GLU* 4.2 1.9 - - - +
671C MET* 3.2 39.8 - - + +
672C GLY 2.7 19.0 + - - -
673C LEU 3.7 0.9 - - - -
674C PRO* 3.6 31.2 - - + +
679C ASN 3.2 23.1 + - - -
680C LEU* 3.4 11.7 - - + +
681C ASP 3.2 0.6 - - - -
682C HIS* 1.3 78.7 - - - +
684C ARG* 1.3 62.1 + - - +
685C ASN 3.5 0.2 + - - -
686C SER* 3.5 10.5 + - - -
687C THR* 3.8 11.4 - - - +
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Residues in contact with ARG 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658C ARG* 3.3 29.2 - - - +
660C GLU* 3.1 30.0 + - - -
680C LEU* 3.1 40.6 + - + +
681C ASP* 4.0 3.6 - - - +
683C TYR* 1.3 76.4 - - - +
685C ASN* 1.3 62.6 + - - +
686C SER 3.4 0.2 + - - -
687C THR* 3.7 20.5 + - - +
690C SER* 4.5 4.5 + - - -
245D SER* 5.9 5.3 + - - -
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Residues in contact with ASN 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638C MET* 5.0 2.6 - - - +
681C ASP* 2.9 20.5 + - - +
682C HIS* 4.1 12.6 - - + +
683C TYR 3.3 0.2 - - - -
684C ARG* 1.3 78.1 - - - +
686C SER* 1.3 57.4 + - - +
687C THR 3.4 2.9 + - - +
690C SER* 4.1 9.0 + - - -
691C ARG* 5.0 7.6 + - - -
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Residues in contact with SER 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C LEU 3.4 18.5 + - - -
599C GLY* 4.7 1.8 - - - -
600C THR* 5.7 2.5 - - - -
634C TYR* 2.7 41.7 + - - -
638C MET* 3.7 11.6 - - - +
657C SER 4.4 0.5 - - - +
658C ARG* 5.4 0.4 - - - -
659C TRP* 3.6 18.9 - - - -
671C MET* 4.3 1.4 - - - +
682C HIS 2.9 20.4 + - - -
683C TYR* 3.5 7.0 + - - -
684C ARG 3.3 0.8 - - - -
685C ASN* 1.3 76.8 - - - +
687C THR* 1.3 62.5 + - - +
691C ARG* 5.8 0.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il